Abstract: Stress is a response of the organism which alters the homeostasis. Role of chronic stress in the modulation of common gastrointestinal disorders has already been established. Long lasting stress affects the synaptic plasticity, dendritic morphology and neurogenesis. The present study was conducted to evaluate the morphological changes in the enteric nervous system of rat colon to understand the basis of functional and physiological alterations in response to chronic stress. Seven male wistar rats were subjected to chronic passive avoidance stress for 6 hours daily for 42 days and they were compared with equal number of controls. Colonic tissue was collected for histochemistry of nitrergic and cholinergic neurons of myenteric plexus of enteric nervous system and evaluated both by light and electron microscope. The number and size of the neurons were evaluated. The area, perimeter and maximum diameter or ferret diameter were measured according to the principles of stereology for neuronal profile. There was atrophy of both nitrergic and cholinergic neurons as well as reduction in number in the myenteric plexus in rat colon. There were bouts of diarrhoea followed by constipation in the stressed animals. Psychological stress is known to cause oxidative stress to the cells, which damages the DNA structure leading to cell death. Thus apoptosis could be responsible for reduction of neuronal cell population and size. The dismotility may be due to imbalance between inhibitory (nitrergic) and excitatory (cholinergic) neurons due to their atrophy.